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Question: Selection of terms in clusterProfiler, the inverse of dropGO
0
gravatar for Sebastian Hesse
16 days ago by
Germany / Munich / Dr.von Hauner Children's Hospital
Sebastian Hesse30 wrote:

The clusterProfiler package has the function dropGO to exclude terms from the plotting but is there also a method so select the terms one wants to show?

Im asking because in my cellular component enrichment I have multiple occurrences of eg granule subsets and would specifically choose only non redundant ones (simplify unfortunately can not differentiate here enough to exclude overlaps).

I tried the following:

 excludeCCdown <- down_CC@compareClusterResult$Description
 remove <- c(5, 7, 11, 15, 16, 125) #contains terms I want to keep
 excludeCCdown <- excludeCCdown[! excludeCCdown %in% remove]
 granules_CC_down <- dropGO(down_CC, term = excludeCCdown)

However, the resulting granulesCCdown still contains all the dropped terms.

Thanks for your help! Sebastian

clusterprofiler R • 95 views
ADD COMMENTlink modified 16 days ago • written 16 days ago by Sebastian Hesse30
Answer: Selection of terms in clusterProfiler, the inverse of dropGO
1
gravatar for Sebastian Hesse
16 days ago by
Germany / Munich / Dr.von Hauner Children's Hospital
Sebastian Hesse30 wrote:

Ok, I found a workaround:

excludeCCdown <- data.frame("ID" = down_CC@compareClusterResult$ID, "name" = down_CC@compareClusterResult$Description)
remove <- c("GO:0099503", "GO:0042582", "GO:0042581", "GO:0070820 ", "GO:0101002") #secretory vesicle, azurophil granule, specific granule, tertiary granule, ficolin-1-rich granule
excludeCCdown <- excludeCCdown$ID[! excludeCCdown$ID %in% remove]

granules_CC_down <- dropGO(down_CC, term = excludeCCdown)

So dropGO only uses IDs, not terms. One has to extract all terms with ther IDs into a df and choose from there which IDs to keep aka remove from the list of terms to be dropped. Then all works fine.

ADD COMMENTlink written 16 days ago by Sebastian Hesse30
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